Content-Type: multipart/alternative; boundary="----=_NextPart_001_00B3_01C7FEC7.FF6514B0" ------=_NextPart_001_00B3_01C7FEC7.FF6514B0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Thanks for reply, Once you run APBS software in pymol, then you go to visualization part and set molecular surface to -10 to 10 and then you get surface map showing blue, red and white patches (as shown below) . I like to know surface area of each part (blue, red and white). Is it possible to get that? Regards, Chirag Mehta PhD Student Chemical Engineering Department, The University of Queensland, Australia Office: +61-7-33461409 -----Original Message----- From: sobolevnrm@gmail.com [mailto:sobolevnrm@gmail.com] On Behalf Of Nathan Baker Sent: Thursday, 20 September 2007 1:36 AM To: Chirag Mehta Cc: apbs-users@lists.sourceforge.net Subject: Re: [Apbs-users] Electrostatic calculation Hello -- Do you really want a charge map or an electrostatic potential map? In the case of the latter, the steps to display the surface map are described here http://apbs.sourceforge.net/doc/tutorial/index.html#pymol-sect for PyMOL and here http://apbs.sourceforge.net/doc/tutorial/index.html#viz-sect for other visualization software. Good luck, Nathan On 9/18/07, Chirag Mehta wrote: > > > > > Dear all, > > > > I am new to molecular simulation. Recently I have used PYMOL and APBS > combination to generate electrostatic charge map in salt environment. I like > to know if it's possible to calculate surface positive and negative charge > once APBS generates charge map. > > > > Regards, > > > > Chirag Mehta > > PhD Student > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > apbs-users mailing list > apbs-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ------=_NextPart_001_00B3_01C7FEC7.FF6514B0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Thanks for reply,

 

Once you run APBS software in pymol, then you go to = visualization part and set molecular surface to -10 to 10 and then you get surface map = showing blue, red and white patches (as shown below) . I like to know surface = area of each part (blue, red and white). Is it possible to get = that?

 

 

Regards,

 

Chirag Mehta

PhD Student

Chemical Engineering Department,

The University of = Queensland, Australia<= /font>

Office: +61-7-33461409

 

-----Original Message-----
From: sobolevnrm@gmail.com [mailto:sobolevnrm@gmail.com] On Behalf Of = Nathan Baker
Sent: Thursday, 20 September 2007 1:36 AM
To: Chirag Mehta
Cc: apbs-users@lists.sourceforge.net
Subject: Re: [Apbs-users] Electrostatic calculation

 

Hello --

 

Do you really want a charge map or an electrostatic potential map?  In

the case of the latter, the steps to display the surface map = are

described here

 

    http://apbs.sourceforge.net/doc/tutorial/index.html#pymol-sect=

 

for PyMOL and here

 

    http://apbs.sourceforge.net/doc/tutorial/index.html#viz-sect

 

for other visualization software.

 

Good luck,

 

Nathan

 

On 9/18/07, Chirag Mehta <c.mehta@uq.edu.au> = wrote:

> 

> 

> 

> 

> Dear all,

> 

> 

> 

> I am new to molecular simulation. Recently I have used = PYMOL and APBS

> combination to generate electrostatic charge map in salt environment. I like

> to know if it's possible to calculate surface positive and negative charge

> once APBS generates charge = map.

> 

> 

> 

> Regards,

> 

> 

> 

> Chirag Mehta

> 

> PhD Student

> 

> 

> -------------------------------------------------------------------------=

> This SF.net email is sponsored by: = Microsoft

> Defy all challenges. Microsoft(R) Visual Studio = 2005.

> = http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/=

> = _______________________________________________<= /p>

> apbs-users mailing list

> = apbs-users@lists.sourceforge.net

> = https://lists.sourceforge.net/lists/listinfo/apbs-users=

> 

> 

 

 

--

Associate Professor, Dept. of Biochemistry and Molecular = Biophysics

Center for Computational Biology, Washington University in St. = Louis

Web: http://cholla.wustl.edu/

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